Do you perhaps have an operating system which is not set to US English as default language?
I am working with a set-up almost exactly as you have, and have been struggling with a similar problem since I upgraded MinGW to 4.6.2.

Normally, CDT should detect the installation of MinGW and also auto-discover include configurations and symbols when you build a project.
There should be no need to manually add those standard include paths.

The way CDT does this is by compiling a small file, and analyzing the output of the compiler.
It then extracts all necessary compiler configuration from this output, e.g. include-paths and symbols.
You can find these option under: "(Project) Properties -> C/C++ Build -> Discovery Options".

Since a few versions ago (I don't know the exact one), MinGW enabled support for localized compiler output.
If you are running a French operating system, you will get French compiler warnings and messages.

CDT doesn't like this; it's auto-discovery becomes broken, and you are left with an editor which doesn't know about the standard library includes.

To fix this, I forced the compiler to use English output when building:
Under "Window -> Preferences -> C/C++ -> Build -> Environment", add two new environment variables "LANG" and "LC_ALL" and set them both to "en_US".

Rebuild your project, and CDT should discover the correct include paths again.